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Adapters now also return lattice information for structures that are periodic in 1 or 2 dimensions. #1233

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JPBergsma
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This PR fixes a bug in testing whether fractional coordinates are generated correctly, and enables the returning of lattice information in the pymatgen, proteindatabank and cif adapters for structures that are periodic in less than three dimensions.

closes #1232 closes #1212

…al_coordinates function are generated correctly. 2. Added support to the cif, pymatgen and proteindatabank adapters for generating lattice data for structures that are not periodic in all three dimensions.
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codecov bot commented Jun 9, 2022

Codecov Report

Merging #1233 (6c64244) into master (88860c4) will increase coverage by 0.08%.
The diff coverage is 92.30%.

@@            Coverage Diff             @@
##           master    #1233      +/-   ##
==========================================
+ Coverage   90.81%   90.90%   +0.08%     
==========================================
  Files          72       72              
  Lines        4357     4364       +7     
==========================================
+ Hits         3957     3967      +10     
+ Misses        400      397       -3     
Flag Coverage Δ
project 90.90% <92.30%> (+0.08%) ⬆️
validator 90.90% <92.30%> (+0.08%) ⬆️

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Impacted Files Coverage Δ
optimade/adapters/structures/utils.py 83.84% <85.71%> (+2.54%) ⬆️
optimade/adapters/structures/cif.py 100.00% <100.00%> (ø)
optimade/adapters/structures/proteindatabank.py 100.00% <100.00%> (ø)
optimade/adapters/structures/pymatgen.py 98.66% <100.00%> (ø)
optimade/adapters/structures/ase.py 100.00% <0.00%> (+2.70%) ⬆️

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…rk under python 3.7. Also nperiodic_dimensions is now calculated in the function null_lattice_vector_structure.
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ml-evs commented Jul 6, 2022

Perhaps @CasperWA could take a look at this if he has time? I think this fix is primarily related to how the mcloud client uses the adapters (also pinging @unkcpz in case you want to test this PR out directly Jusong!)

@ml-evs ml-evs mentioned this pull request Jul 16, 2022
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Well, there's no objections from anyone else, so this is fine with me. Thanks @JPBergsma

@JPBergsma JPBergsma merged commit 58ea2cc into Materials-Consortia:master Aug 27, 2022
@JPBergsma JPBergsma deleted the JPBergsma/return_2d_lattice branch August 27, 2022 11:00
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